Acid-Base Catalysis in Designed Peptides

Baltzer s group has recently described a fully-synthetic protein that is also capable of hydrolysing p-nitrophenyl esters the polypeptide, which contains 42 amino acids, was designed to fold into a hairpin helix-loop-helix motif that dimerises into a four-helix bundle. The dimer is predicted to present on its surface a shallow reactive site containing several histidine residues. The spectroscopic properties of the peptide are consistent with the predicted folded structure, and the molecule does indeed catalyse ester hydrolysis (and transesterification) more effectively than 4-methylimidazole does. However, there is little substrate selectivity, and not much turnover. The histidine array does not seem to act via general acid-base catalysis, but rather to bind and stabilise ester oxygens in the transition state. We return to this molecule below. 

Mechanism-based enzyme inactivators are also powerful tools in the determination of enzyme mechanisms. Because some understanding of the enzyme mechanism is required for the design of an inactivator, the success of the compound provides support for the mechanistic hypothesis. Analysis of the intermediates and products of an inactivation reaction can be extremely useful in illuminating the normal mechanism of enzymic catalysis. For example, the covalent modification of an enzyme by a mechanism-based inactivator facilitates isolation of active site peptides and identification of cataiytically relevant amino acids. 

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